Network analysis of pseudogene-gene relationships: from pseudogene evolution to their functional potentials
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Pseudogene
Transcription factor pseudogenes have not been systematically studied before. Nuclear receptors (NRs) constitute one of the largest groups of transcription factors in animals (e.g., 48 NRs in human). The availability of whole-genome sequences enables a global inventory of the NR pseudogenes in a number of vertebrate model organisms. Here we identify the NR pseudogenes in 8 vertebrate organisms and make our results available online at http://www.pseudogene.org/nr. The assignments reveal that NR pseudogenes as a group have characteristics related to generation and distribution contrary to expectations derived from previous large-scale pseudogene studies. In particular, 1) despite its large size, the NR gene family has only a very small number of pseudogenes in each of the vertebrate genomes examined; 2) despite the low transcription levels of NR genes, except for one, all other NR pseudogenes identified in this study are retropseudogenes; and 3) no duplicated NR pseudogenes are found, contrary to the fact that the NR gene family was expanded through several waves of gene duplication events. Our analyses further reveal a number of interesting aspects of NR pseudogenes. Specifically, through careful sequence analysis, we identify remnant introns in 2 mouse retropseudogenes, ψRev-erbβ and ψLRH1. Generated from partially processed pre-mRNAs, they appear to be rare examples of highly unusual "semiprocessed" pseudogenes. Second, by comparing the genomic sequences, we uncover a pseudogene that is unique to the human lineage relative to chimpanzee. Generated by a recent duplication of a segment in the human genome, this pseudogene is a "duplicated–processed" pseudogene, belonging to a new pseudogene species. Finally, FXRβ was nonfunctionalized in the human lineage and thus appears to be an example of a rare unitary pseudogene. By comparing orthologous sequences, we dated the FXR–FXRβ duplication and the nonfunctionalization of FXRβ in primates.
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In this report 118 mouse Vκ genes are described which, together with the 22 Vκ genes reported previously (T. Kirschbaum et al., Eur. J. Immunol. 1998. 28: 1458 – 1466) amount to 140 genes that had been cloned and sequenced in our laboratory. For 73 of them cDNAs are known, i. e. they have to be considered functional genes, although 10 genes of this group have 1-bp deviations from the canonical promoter, splice site or heptanucleotide recombination signal sequences. Twenty Vκ genes have been defined as only potentially functional since they do not contain any defect, but no cDNAs have been found (yet) for them. Of the 140 Vκ genes 47 are pseudogenes. There are indications that two to five Vκ genes or pseudogenes exist in the κ locus which we have not yet been able to clone. The 140 Vκ genes and pseudogenes were assigned to 18 gene families, 4 of them being one-member families. This differs from previous enumerations of the families only by the combination of the Vκ9 and Vκ10 families and by the addition of the Vκdv gene as a new separate family. Sequence identity usually was 80 % or above within the gene families and 55 – 80 % between genes of different families. Many of the mouse Vκ gene families show significant homologies to the human ones, indicating that in evolution Vκ gene diversification predated the divergence of the primate and rodent clades.
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Avian infectious bronchitis
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Ribosomal protein
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To study the variation of procine reproductive and respiratory syndrome virus(PRRSV),three PRRSV isolates(TJ-S1,TJ-S2 and TJ-S3) were obtained from Tianjin province's pig farms.A pair of primers were designed according to the published sequence of Nsp2 gene of BJ-4 strain and used to amplify the partial Nsp2 gene by RT-PCR,the PCR products were cloned into pGEM-T vector and then sequenced.The sequence was analyzed by DNAstar software.Sequence and phylogenetic analysis showed that all these 3 isolates belong to the North American genotype,TJ-S1 strain and TJ-S2 strain shared a common feature of distinctive deletions in 221 and 272-300 amino acids.The phylogenetic tree revealed that TJ-S1 strain,TJ-S2 strain had close relationship with HuN strain and SD-14 strain,TJ-S3 was close to CH-1a.
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Pseudogenes are fossil relatives of genes. Pseudogenes have long been thought of as junk DNAs, since they do not code proteins in normal tissues. Although most of the human pseudogenes do not have noticeable functions, ∼20% of them exhibit transcriptional activity. There has been evidence showing that some pseudogenes adopted functions as lncRNAs and work as regulators of gene expression. Furthermore, pseudogenes can even be reactivated in some conditions, such as cancer initiation. Some pseudogenes are transcribed in specific cancer types, and some are even translated into proteins as observed in several cancer cell lines. All the above have shown that pseudogenes could have functional roles or potentials in the genome. Evaluating the relationships between pseudogenes and their gene counterparts could help us reveal the evolutionary path of pseudogenes and associate pseudogenes with functional potentials. It also provides an insight into the regulatory networks involving pseudogenes with transcriptional and even translational activities.In this study, we develop a novel approach integrating graph analysis, sequence alignment and functional analysis to evaluate pseudogene-gene relationships, and apply it to human gene homologs and pseudogenes. We generated a comprehensive set of 445 pseudogene-gene (PGG) families from the original 3,281 gene families (13.56%). Of these 438 (98.4% PGG, 13.3% total) were non-trivial (containing more than one pseudogene). Each PGG family contains multiple genes and pseudogenes with high sequence similarity. For each family, we generate a sequence alignment network and phylogenetic trees recapitulating the evolutionary paths. We find evidence supporting the evolution history of olfactory family (both genes and pseudogenes) in human, which also supports the validity of our analysis method. Next, we evaluate these networks in respect to the gene ontology from which we identify functions enriched in these pseudogene-gene families and infer functional impact of pseudogenes involved in the networks. This demonstrates the application of our PGG network database in the study of pseudogene function in disease context.
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Pseudogenes,disabled copies of functional genes,are structurally similar to its parantal genes,but lost their ability to produce proteins.Pseudogene was used to be considered as a typical kind of non-codingjunk DNA.Increasing investigations,however,have shown that pseudogenes play important roles in gene regulation and genome evolution.The progress of research on pseudogenes is summarized in light of the origin and sequence characteristics of pseudogenes,identification of pseudogenes,genomic distribution,behaviour of its molecular evolution and functioning.
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